from setuptools import setup

def readme():
    with open('README.md', encoding="utf-8") as f:
        return f.read()

setup(
    name='scTE',
    use_scm_version=True,
    setup_requires=['setuptools_scm'],
    description='Quantifying transposable element (TEs) expression from single-cell sequencing data',
    long_description=readme(),
    long_description_content_type='text/markdown',
    classifiers=[
        'Programming Language :: Python :: 3',
        'Programming Language :: Python :: 3.9',  # Updated to match meta.yaml
        'License :: OSI Approved :: MIT License',
        'Operating System :: POSIX :: Linux',
        'Operating System :: MacOS :: MacOS X',
    ],
    python_requires=">=3.9",  # Updated to match meta.yaml
    url='https://gitee.com/Billsfriend/scTE',
    author='Jiangping He, Andrew P. Hutchins',
    author_email='he_jiangping@grmh-gdl.cn, andrewh@sustech.edu.cn',
    packages=[
        'scTE',
        'scTE.miniglbase',
    ],
    platforms=[
        'Linux',
        'MacOS'
    ],
    include_package_data=True,
    zip_safe=False,
    scripts=[
        'bin/scTE',
        'bin/scTE_build',
        'bin/scTEATAC_build',
        'bin/scTEATAC',
    ]
)
